PCNX1

pecanex 1

Basic information

Region (hg38): 14:70907404-71115382

Previous symbols: [ "PCNXL1", "PCNX" ]

Links

ENSG00000100731 ∙ NCBI:22990 ∙ OMIM:617655 ∙ HGNC:19740 ∙ Uniprot:Q96RV3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCNX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNX1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	5	10
missense			19	3	4	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	19	8	10

Variants in PCNX1

This is a list of pathogenic ClinVar variants found in the PCNX1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-70907862-G-C		not specified	Uncertain significance (Nov 16, 2021)
14-70907901-C-T			Likely benign (Apr 01, 2022)
14-70946990-G-A		not specified	Uncertain significance (Sep 01, 2021)
14-70946994-A-C			Benign (Oct 09, 2018)
14-70947065-C-G			Likely benign (Apr 01, 2022)
14-70976988-C-T			Likely benign (Apr 30, 2018)
14-70977031-T-C			Likely benign (Jun 01, 2022)
14-70977098-C-G		not specified	Uncertain significance (Nov 08, 2021)
14-70977099-T-G			Benign (Jan 01, 2023)
14-70977260-G-A		not specified	Uncertain significance (Nov 15, 2021)
14-70977684-T-C			Benign (Jul 04, 2018)
14-70977710-C-T		not specified	Likely benign (Oct 27, 2021)
14-70977749-C-G			Benign (Dec 31, 2019)
14-70978076-A-G		not specified	Uncertain significance (Nov 16, 2021)
14-70978120-A-C		not specified	Uncertain significance (Jun 11, 2021)
14-70978353-G-A			Benign (Dec 31, 2019)
14-70978354-C-T		not specified	Uncertain significance (Nov 09, 2021)
14-70978516-G-C		not specified	Uncertain significance (Nov 12, 2021)
14-70978539-A-G			Benign (May 03, 2018)
14-70988600-G-A			Likely benign (May 18, 2018)
14-70988677-T-C			Benign (Oct 09, 2018)
14-70988692-C-T		not specified	Uncertain significance (Oct 29, 2021)
14-71009651-C-G		not specified	Uncertain significance (Jul 27, 2021)
14-71019061-G-T		Malignant tumor of prostate	Uncertain significance (-)
14-71033444-C-G		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCNX1	protein_coding	protein_coding	ENST00000304743	36	207978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000139	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	1124	1.27e+3	0.887	0.0000687	15288
Missense in Polyphen		408	579.56	0.70398		6918
Synonymous	-0.375	474	464	1.02	0.0000236	4690
Loss of Function	8.35	17	113	0.151	0.00000674	1259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.000404	0.000397
East Asian	0.000218	0.000163
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.000218	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -1.95
• rvis_percentile_EVS: 1.87

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.466
• ghis: 0.595

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pcnx

Gene ontology

• Cellular component: integral component of membrane